Starting phenix.real_space_refine on Tue Sep 24 03:51:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx2_37898/09_2024/8wx2_37898.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx2_37898/09_2024/8wx2_37898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx2_37898/09_2024/8wx2_37898.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx2_37898/09_2024/8wx2_37898.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx2_37898/09_2024/8wx2_37898.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx2_37898/09_2024/8wx2_37898.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 4528 2.51 5 N 1110 2.21 5 O 1126 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6800 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3400 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 23, 'TRANS': 416} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Restraints were copied for chains: B Time building chain proxies: 6.05, per 1000 atoms: 0.89 Number of scatterers: 6800 At special positions: 0 Unit cell: (128.65, 88.81, 81.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1126 8.00 N 1110 7.00 C 4528 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 526 " - pdb=" SG CYS A 536 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 1.1 seconds 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1624 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 0 sheets defined 86.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 30 through 63 Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.913A pdb=" N GLN A 71 " --> pdb=" O THR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 98 removed outlier: 3.555A pdb=" N VAL A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 100 through 123 removed outlier: 3.601A pdb=" N VAL A 104 " --> pdb=" O ARG A 100 " (cutoff:3.500A) Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 123 through 131 removed outlier: 3.730A pdb=" N ARG A 127 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 191 Processing helix chain 'A' and resid 191 through 224 removed outlier: 3.774A pdb=" N ILE A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 247 Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 304 through 322 removed outlier: 3.700A pdb=" N PHE A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A 311 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 315 " --> pdb=" O GLN A 311 " (cutoff:3.500A) Proline residue: A 318 - end of helix Processing helix chain 'A' and resid 322 through 343 removed outlier: 3.826A pdb=" N TYR A 326 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLN A 332 " --> pdb=" O MET A 328 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET A 333 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL A 338 " --> pdb=" O GLN A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 393 removed outlier: 3.811A pdb=" N LEU A 375 " --> pdb=" O PRO A 371 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LEU A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 387 " --> pdb=" O VAL A 383 " (cutoff:3.500A) Proline residue: A 388 - end of helix Processing helix chain 'A' and resid 393 through 401 removed outlier: 3.537A pdb=" N LEU A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 439 removed outlier: 3.643A pdb=" N TYR A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 436 " --> pdb=" O ARG A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 460 Processing helix chain 'A' and resid 461 through 474 Processing helix chain 'A' and resid 476 through 484 Processing helix chain 'A' and resid 491 through 517 removed outlier: 3.765A pdb=" N MET A 496 " --> pdb=" O GLN A 492 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER A 503 " --> pdb=" O PHE A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 532 Processing helix chain 'A' and resid 537 through 564 removed outlier: 3.541A pdb=" N GLU A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 63 Processing helix chain 'B' and resid 67 through 71 removed outlier: 3.913A pdb=" N GLN B 71 " --> pdb=" O THR B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 98 removed outlier: 3.555A pdb=" N VAL B 78 " --> pdb=" O ARG B 74 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 100 through 123 removed outlier: 3.602A pdb=" N VAL B 104 " --> pdb=" O ARG B 100 " (cutoff:3.500A) Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 123 through 131 removed outlier: 3.730A pdb=" N ARG B 127 " --> pdb=" O PHE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 191 Processing helix chain 'B' and resid 191 through 224 removed outlier: 3.774A pdb=" N ILE B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 247 Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 304 through 322 removed outlier: 3.700A pdb=" N PHE B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN B 311 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS B 315 " --> pdb=" O GLN B 311 " (cutoff:3.500A) Proline residue: B 318 - end of helix Processing helix chain 'B' and resid 322 through 343 removed outlier: 3.827A pdb=" N TYR B 326 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN B 332 " --> pdb=" O MET B 328 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET B 333 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 335 " --> pdb=" O PHE B 331 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL B 338 " --> pdb=" O GLN B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 393 removed outlier: 3.811A pdb=" N LEU B 375 " --> pdb=" O PRO B 371 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LEU B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL B 383 " --> pdb=" O ASN B 379 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 387 " --> pdb=" O VAL B 383 " (cutoff:3.500A) Proline residue: B 388 - end of helix Processing helix chain 'B' and resid 393 through 401 removed outlier: 3.537A pdb=" N LEU B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 439 removed outlier: 3.644A pdb=" N TYR B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 436 " --> pdb=" O ARG B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 460 Processing helix chain 'B' and resid 461 through 474 Processing helix chain 'B' and resid 476 through 484 Processing helix chain 'B' and resid 491 through 517 removed outlier: 3.764A pdb=" N MET B 496 " --> pdb=" O GLN B 492 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER B 503 " --> pdb=" O PHE B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 537 through 564 removed outlier: 3.540A pdb=" N GLU B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1566 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.25 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2080 1.35 - 1.47: 1782 1.47 - 1.59: 3062 1.59 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6982 Sorted by residual: bond pdb=" C ALA A 487 " pdb=" N PRO A 488 " ideal model delta sigma weight residual 1.334 1.369 -0.036 2.34e-02 1.83e+03 2.31e+00 bond pdb=" C ALA B 487 " pdb=" N PRO B 488 " ideal model delta sigma weight residual 1.334 1.368 -0.034 2.34e-02 1.83e+03 2.17e+00 bond pdb=" C LEU B 519 " pdb=" N PRO B 520 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 7.99e-01 bond pdb=" C LEU A 519 " pdb=" N PRO A 520 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.36e-01 bond pdb=" CA THR B 248 " pdb=" C THR B 248 " ideal model delta sigma weight residual 1.524 1.534 -0.010 1.26e-02 6.30e+03 6.63e-01 ... (remaining 6977 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 9274 1.57 - 3.14: 162 3.14 - 4.70: 55 4.70 - 6.27: 19 6.27 - 7.84: 12 Bond angle restraints: 9522 Sorted by residual: angle pdb=" N PRO A 351 " pdb=" CA PRO A 351 " pdb=" CB PRO A 351 " ideal model delta sigma weight residual 103.00 110.44 -7.44 1.10e+00 8.26e-01 4.58e+01 angle pdb=" N PRO B 351 " pdb=" CA PRO B 351 " pdb=" CB PRO B 351 " ideal model delta sigma weight residual 103.00 110.41 -7.41 1.10e+00 8.26e-01 4.53e+01 angle pdb=" N ALA A 487 " pdb=" CA ALA A 487 " pdb=" C ALA A 487 " ideal model delta sigma weight residual 109.81 117.65 -7.84 2.21e+00 2.05e-01 1.26e+01 angle pdb=" N ALA B 487 " pdb=" CA ALA B 487 " pdb=" C ALA B 487 " ideal model delta sigma weight residual 109.81 117.60 -7.79 2.21e+00 2.05e-01 1.24e+01 angle pdb=" N ARG B 74 " pdb=" CA ARG B 74 " pdb=" CB ARG B 74 " ideal model delta sigma weight residual 114.17 110.48 3.69 1.14e+00 7.69e-01 1.05e+01 ... (remaining 9517 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.95: 3527 14.95 - 29.91: 337 29.91 - 44.86: 126 44.86 - 59.81: 36 59.81 - 74.77: 4 Dihedral angle restraints: 4030 sinusoidal: 1504 harmonic: 2526 Sorted by residual: dihedral pdb=" CA ALA B 487 " pdb=" C ALA B 487 " pdb=" N PRO B 488 " pdb=" CA PRO B 488 " ideal model delta harmonic sigma weight residual -180.00 -135.20 -44.80 0 5.00e+00 4.00e-02 8.03e+01 dihedral pdb=" CA ALA A 487 " pdb=" C ALA A 487 " pdb=" N PRO A 488 " pdb=" CA PRO A 488 " ideal model delta harmonic sigma weight residual -180.00 -135.27 -44.73 0 5.00e+00 4.00e-02 8.00e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 157 " pdb=" CB CYS A 157 " ideal model delta sinusoidal sigma weight residual -86.00 -28.57 -57.43 1 1.00e+01 1.00e-02 4.43e+01 ... (remaining 4027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 917 0.049 - 0.098: 166 0.098 - 0.147: 25 0.147 - 0.196: 0 0.196 - 0.245: 2 Chirality restraints: 1110 Sorted by residual: chirality pdb=" CA PRO B 351 " pdb=" N PRO B 351 " pdb=" C PRO B 351 " pdb=" CB PRO B 351 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA PRO A 351 " pdb=" N PRO A 351 " pdb=" C PRO A 351 " pdb=" CB PRO A 351 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA PRO B 488 " pdb=" N PRO B 488 " pdb=" C PRO B 488 " pdb=" CB PRO B 488 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 1107 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 487 " 0.048 5.00e-02 4.00e+02 7.35e-02 8.64e+00 pdb=" N PRO A 488 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 488 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 488 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 487 " -0.048 5.00e-02 4.00e+02 7.32e-02 8.57e+00 pdb=" N PRO B 488 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 488 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 488 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 118 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO B 119 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 119 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 119 " 0.026 5.00e-02 4.00e+02 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 50 2.61 - 3.18: 6070 3.18 - 3.75: 11342 3.75 - 4.33: 14422 4.33 - 4.90: 23139 Nonbonded interactions: 55023 Sorted by model distance: nonbonded pdb=" SG CYS B 526 " pdb=" SG CYS B 536 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS B 131 " pdb=" SG CYS B 157 " model vdw 2.034 3.760 nonbonded pdb=" N ASN A 66 " pdb=" OD1 ASN A 66 " model vdw 2.171 3.120 nonbonded pdb=" N ASN B 66 " pdb=" OD1 ASN B 66 " model vdw 2.171 3.120 nonbonded pdb=" O PHE B 65 " pdb=" N THR B 68 " model vdw 2.206 3.120 ... (remaining 55018 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.430 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6982 Z= 0.145 Angle : 0.646 7.841 9522 Z= 0.357 Chirality : 0.038 0.245 1110 Planarity : 0.005 0.074 1172 Dihedral : 14.514 74.766 2400 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.51 % Favored : 93.02 % Rotamer: Outliers : 1.99 % Allowed : 14.25 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.26), residues: 860 helix: -0.96 (0.18), residues: 680 sheet: None (None), residues: 0 loop : -3.01 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 67 HIS 0.001 0.000 HIS B 434 PHE 0.011 0.001 PHE A 65 TYR 0.013 0.001 TYR B 59 ARG 0.001 0.000 ARG B 489 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 157 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.5625 (mtm-85) cc_final: 0.5291 (mtp180) REVERT: A 460 TRP cc_start: 0.5111 (m-90) cc_final: 0.4845 (m-10) outliers start: 14 outliers final: 8 residues processed: 169 average time/residue: 0.1734 time to fit residues: 39.3533 Evaluate side-chains 117 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 526 CYS Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 526 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 44 optimal weight: 10.0000 chunk 35 optimal weight: 0.0870 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 79 optimal weight: 0.0030 overall best weight: 0.5168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN B 178 ASN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6982 Z= 0.209 Angle : 0.765 10.055 9522 Z= 0.371 Chirality : 0.042 0.149 1110 Planarity : 0.006 0.074 1172 Dihedral : 6.574 59.304 950 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.85 % Allowed : 18.95 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.28), residues: 860 helix: 0.27 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -2.86 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 558 HIS 0.006 0.002 HIS B 434 PHE 0.023 0.001 PHE A 244 TYR 0.025 0.001 TYR A 59 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 124 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 PHE cc_start: 0.6691 (t80) cc_final: 0.6130 (t80) REVERT: A 374 TRP cc_start: 0.5797 (t60) cc_final: 0.5413 (t60) REVERT: A 460 TRP cc_start: 0.5054 (m-90) cc_final: 0.4370 (m100) REVERT: B 460 TRP cc_start: 0.5125 (m-90) cc_final: 0.4824 (m-10) outliers start: 27 outliers final: 15 residues processed: 139 average time/residue: 0.1557 time to fit residues: 29.8794 Evaluate side-chains 128 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 113 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 526 CYS Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 332 GLN Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 398 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 66 optimal weight: 0.0170 chunk 54 optimal weight: 20.0000 chunk 22 optimal weight: 0.5980 chunk 80 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 79 optimal weight: 0.0000 chunk 27 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 overall best weight: 0.4822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 HIS B 343 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6982 Z= 0.193 Angle : 0.735 10.926 9522 Z= 0.353 Chirality : 0.042 0.154 1110 Planarity : 0.006 0.074 1172 Dihedral : 6.334 58.399 947 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 4.13 % Allowed : 20.09 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.29), residues: 860 helix: 0.55 (0.19), residues: 720 sheet: None (None), residues: 0 loop : -3.51 (0.48), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 204 HIS 0.006 0.001 HIS B 434 PHE 0.026 0.002 PHE A 202 TYR 0.013 0.001 TYR A 59 ARG 0.004 0.000 ARG A 537 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 117 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 PHE cc_start: 0.6830 (OUTLIER) cc_final: 0.6547 (m-80) REVERT: A 374 TRP cc_start: 0.5861 (t60) cc_final: 0.5457 (t60) REVERT: A 460 TRP cc_start: 0.5135 (m-90) cc_final: 0.4496 (m100) REVERT: A 486 GLU cc_start: 0.5420 (pm20) cc_final: 0.5145 (mp0) REVERT: B 74 ARG cc_start: 0.2730 (OUTLIER) cc_final: 0.0073 (ttt180) REVERT: B 198 PHE cc_start: 0.6599 (t80) cc_final: 0.6060 (t80) REVERT: B 219 PHE cc_start: 0.6779 (OUTLIER) cc_final: 0.6472 (m-80) REVERT: B 460 TRP cc_start: 0.5085 (m-90) cc_final: 0.4369 (m100) outliers start: 29 outliers final: 12 residues processed: 131 average time/residue: 0.1571 time to fit residues: 28.7985 Evaluate side-chains 113 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 526 CYS Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 398 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 53 optimal weight: 0.0030 chunk 80 optimal weight: 10.0000 chunk 85 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6982 Z= 0.204 Angle : 0.760 12.528 9522 Z= 0.362 Chirality : 0.042 0.178 1110 Planarity : 0.006 0.075 1172 Dihedral : 5.661 44.149 943 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.99 % Allowed : 19.94 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.29), residues: 860 helix: 0.94 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -3.16 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 558 HIS 0.003 0.001 HIS A 434 PHE 0.020 0.001 PHE A 244 TYR 0.028 0.001 TYR B 59 ARG 0.004 0.000 ARG B 537 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 105 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 PHE cc_start: 0.6807 (OUTLIER) cc_final: 0.6523 (m-80) REVERT: A 460 TRP cc_start: 0.5232 (m-90) cc_final: 0.4602 (m100) REVERT: B 74 ARG cc_start: 0.2689 (OUTLIER) cc_final: 0.0050 (ttt180) REVERT: B 219 PHE cc_start: 0.6619 (OUTLIER) cc_final: 0.6344 (m-80) REVERT: B 460 TRP cc_start: 0.5164 (m-90) cc_final: 0.4482 (m100) outliers start: 35 outliers final: 16 residues processed: 127 average time/residue: 0.1707 time to fit residues: 29.3603 Evaluate side-chains 114 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 438 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.0870 chunk 1 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 72 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 76 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6982 Z= 0.197 Angle : 0.767 13.110 9522 Z= 0.364 Chirality : 0.042 0.184 1110 Planarity : 0.005 0.072 1172 Dihedral : 5.582 44.632 942 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.85 % Allowed : 22.51 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.29), residues: 860 helix: 1.20 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -3.28 (0.44), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 558 HIS 0.002 0.001 HIS B 343 PHE 0.021 0.001 PHE A 244 TYR 0.022 0.001 TYR B 59 ARG 0.007 0.001 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 110 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 PHE cc_start: 0.6513 (t80) cc_final: 0.5978 (t80) REVERT: A 219 PHE cc_start: 0.6804 (OUTLIER) cc_final: 0.6531 (m-80) REVERT: A 460 TRP cc_start: 0.5177 (m-90) cc_final: 0.4560 (m100) REVERT: B 74 ARG cc_start: 0.2588 (OUTLIER) cc_final: 0.0050 (ttt180) REVERT: B 219 PHE cc_start: 0.6658 (OUTLIER) cc_final: 0.6327 (m-80) REVERT: B 460 TRP cc_start: 0.5113 (m-90) cc_final: 0.4760 (m-10) outliers start: 27 outliers final: 16 residues processed: 123 average time/residue: 0.1579 time to fit residues: 27.1527 Evaluate side-chains 111 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 526 CYS Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 438 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 85 optimal weight: 0.4980 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 0.2980 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6982 Z= 0.212 Angle : 0.790 13.255 9522 Z= 0.374 Chirality : 0.046 0.290 1110 Planarity : 0.005 0.074 1172 Dihedral : 5.499 43.699 942 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.13 % Allowed : 23.50 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.30), residues: 860 helix: 1.32 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -3.67 (0.44), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 558 HIS 0.003 0.001 HIS B 343 PHE 0.020 0.001 PHE B 244 TYR 0.017 0.001 TYR B 59 ARG 0.004 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 103 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 PHE cc_start: 0.6782 (OUTLIER) cc_final: 0.6517 (m-80) REVERT: A 460 TRP cc_start: 0.5273 (m-90) cc_final: 0.4696 (m100) REVERT: B 74 ARG cc_start: 0.2586 (OUTLIER) cc_final: 0.0094 (ttt180) REVERT: B 198 PHE cc_start: 0.6502 (t80) cc_final: 0.5996 (t80) REVERT: B 219 PHE cc_start: 0.6580 (OUTLIER) cc_final: 0.6281 (m-80) REVERT: B 460 TRP cc_start: 0.5244 (m-90) cc_final: 0.4582 (m100) outliers start: 29 outliers final: 19 residues processed: 121 average time/residue: 0.1650 time to fit residues: 27.3366 Evaluate side-chains 114 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 92 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 526 CYS Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 332 GLN Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 438 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 20.0000 chunk 48 optimal weight: 0.3980 chunk 62 optimal weight: 0.0170 chunk 71 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6982 Z= 0.202 Angle : 0.787 13.454 9522 Z= 0.374 Chirality : 0.044 0.186 1110 Planarity : 0.005 0.074 1172 Dihedral : 5.415 44.395 942 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.86 % Favored : 93.02 % Rotamer: Outliers : 4.13 % Allowed : 23.50 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.30), residues: 860 helix: 1.43 (0.20), residues: 718 sheet: None (None), residues: 0 loop : -3.73 (0.43), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 558 HIS 0.002 0.000 HIS B 343 PHE 0.028 0.001 PHE B 202 TYR 0.018 0.001 TYR A 59 ARG 0.004 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 100 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7030 (t80) cc_final: 0.6800 (t80) REVERT: A 219 PHE cc_start: 0.6775 (OUTLIER) cc_final: 0.6508 (m-80) REVERT: A 460 TRP cc_start: 0.5234 (m-90) cc_final: 0.4680 (m100) REVERT: B 74 ARG cc_start: 0.2754 (OUTLIER) cc_final: 0.0318 (ttt180) REVERT: B 198 PHE cc_start: 0.6449 (t80) cc_final: 0.5897 (t80) REVERT: B 219 PHE cc_start: 0.6603 (OUTLIER) cc_final: 0.6253 (m-80) REVERT: B 460 TRP cc_start: 0.5232 (m-90) cc_final: 0.4611 (m100) outliers start: 29 outliers final: 20 residues processed: 117 average time/residue: 0.1555 time to fit residues: 25.5729 Evaluate side-chains 114 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 91 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 526 CYS Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 332 GLN Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 438 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 53 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 0.0970 chunk 77 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6982 Z= 0.208 Angle : 0.801 15.633 9522 Z= 0.378 Chirality : 0.046 0.395 1110 Planarity : 0.005 0.073 1172 Dihedral : 5.375 43.339 942 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.99 % Allowed : 23.36 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.30), residues: 860 helix: 1.46 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -3.55 (0.42), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 558 HIS 0.002 0.000 HIS B 343 PHE 0.017 0.001 PHE A 202 TYR 0.009 0.001 TYR B 59 ARG 0.004 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7058 (t80) cc_final: 0.6789 (t80) REVERT: A 219 PHE cc_start: 0.6776 (OUTLIER) cc_final: 0.6515 (m-80) REVERT: A 460 TRP cc_start: 0.5269 (m-90) cc_final: 0.4738 (m100) REVERT: B 74 ARG cc_start: 0.2838 (OUTLIER) cc_final: 0.0405 (ttt180) REVERT: B 219 PHE cc_start: 0.6561 (OUTLIER) cc_final: 0.6226 (m-80) REVERT: B 460 TRP cc_start: 0.5225 (m-90) cc_final: 0.4634 (m100) outliers start: 28 outliers final: 20 residues processed: 115 average time/residue: 0.1651 time to fit residues: 26.2451 Evaluate side-chains 111 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 88 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 526 CYS Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 332 GLN Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 438 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 34 optimal weight: 0.5980 chunk 62 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6982 Z= 0.223 Angle : 0.810 13.656 9522 Z= 0.384 Chirality : 0.048 0.454 1110 Planarity : 0.006 0.073 1172 Dihedral : 5.399 45.135 942 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 3.13 % Allowed : 24.64 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.30), residues: 860 helix: 1.41 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -3.47 (0.43), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 558 HIS 0.002 0.000 HIS B 343 PHE 0.031 0.001 PHE B 202 TYR 0.011 0.001 TYR A 59 ARG 0.006 0.001 ARG A 562 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 92 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7081 (t80) cc_final: 0.6805 (t80) REVERT: A 219 PHE cc_start: 0.6778 (OUTLIER) cc_final: 0.6518 (m-80) REVERT: A 460 TRP cc_start: 0.5334 (m-90) cc_final: 0.4783 (m100) REVERT: B 74 ARG cc_start: 0.2807 (OUTLIER) cc_final: 0.0419 (ttt180) REVERT: B 198 PHE cc_start: 0.6341 (t80) cc_final: 0.5834 (t80) REVERT: B 460 TRP cc_start: 0.5260 (m-90) cc_final: 0.4659 (m100) outliers start: 22 outliers final: 19 residues processed: 107 average time/residue: 0.1687 time to fit residues: 24.6491 Evaluate side-chains 107 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 86 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 526 CYS Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 332 GLN Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 438 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 69 optimal weight: 0.0000 chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 GLN B 461 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6982 Z= 0.232 Angle : 0.801 13.137 9522 Z= 0.382 Chirality : 0.048 0.432 1110 Planarity : 0.005 0.071 1172 Dihedral : 5.381 42.919 942 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.13 % Allowed : 24.64 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.30), residues: 860 helix: 1.36 (0.20), residues: 730 sheet: None (None), residues: 0 loop : -3.77 (0.45), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 558 HIS 0.002 0.001 HIS B 343 PHE 0.024 0.001 PHE A 198 TYR 0.012 0.001 TYR B 484 ARG 0.004 0.000 ARG A 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7119 (t80) cc_final: 0.6799 (t80) REVERT: A 198 PHE cc_start: 0.6637 (t80) cc_final: 0.6098 (t80) REVERT: A 219 PHE cc_start: 0.6804 (OUTLIER) cc_final: 0.6549 (m-80) REVERT: A 460 TRP cc_start: 0.5357 (m-90) cc_final: 0.4783 (m100) REVERT: B 74 ARG cc_start: 0.2854 (OUTLIER) cc_final: 0.0479 (ttt180) REVERT: B 460 TRP cc_start: 0.5305 (m-90) cc_final: 0.4702 (m100) outliers start: 22 outliers final: 19 residues processed: 111 average time/residue: 0.1645 time to fit residues: 25.2778 Evaluate side-chains 111 residues out of total 720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 438 HIS Chi-restraints excluded: chain A residue 526 CYS Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 332 GLN Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 438 HIS Chi-restraints excluded: chain B residue 491 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 29 optimal weight: 0.0980 chunk 71 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.159953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.136745 restraints weight = 17095.190| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 2.99 r_work: 0.4091 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6982 Z= 0.216 Angle : 0.820 13.681 9522 Z= 0.387 Chirality : 0.048 0.441 1110 Planarity : 0.006 0.102 1172 Dihedral : 5.405 44.928 942 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 2.99 % Allowed : 24.93 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.30), residues: 860 helix: 1.37 (0.20), residues: 730 sheet: None (None), residues: 0 loop : -3.72 (0.46), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 523 HIS 0.002 0.001 HIS B 343 PHE 0.026 0.002 PHE B 198 TYR 0.010 0.001 TYR B 484 ARG 0.006 0.000 ARG A 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1633.02 seconds wall clock time: 29 minutes 41.42 seconds (1781.42 seconds total)